void RunQSNP::run()
{
Configuration* pConfig = Configuration::getConfig();
Logger* pLogger = Logger::getLogger();
pLogger->log(QSNP_ALWAYS, "QualitySNP started with settings: " + pConfig->toString());
ContigProvider contigProvider;
if (!contigProvider.init()) {
emit reportError("Could read contig file");
return;
}
vector<string> readGroups;
if(pConfig->getBool("outputReadGroups")) {
readGroups = contigProvider.getReadGroups();
}
CSVWriter csvWriter(readGroups);
if (!csvWriter.init()) {
emit reportError("Could not write results");
emit done();
return;
}
pConfig->writeFile("config.cfg", pConfig->getString("outputDirectory"));
QString message;
if(pConfig->getBool("collectStatistics")) {
message = QString("Processing a total of %1 contigs with %2 reads").arg(contigProvider.getContigCount()).arg(contigProvider.getReadCount());
emit printMessage(message);
}
QMutex mutex;
Contig* pContig = contigProvider.nextContig();
while (pContig != NULL && !_bCancelled) {
message = "Processing: " + QString::fromStdString(pContig->getName());
emit printMessage(message);
QSNPRunTask *runTask = new QSNPRunTask();
runTask->setContig(pContig);
runTask->setWriter(&csvWriter);
runTask->setShowContigsWithoutSNP(pConfig->getBool("showContigsWithoutSNP"));
runTask->setMutex(&mutex);
while(!QThreadPool::globalInstance()->tryStart(runTask)) {
I::msleep(1); // sleep for 1 millisecond before trying again
}
message = "Done";
emit printMessage(message);
pContig = contigProvider.nextContig();
}
QThreadPool::globalInstance()->waitForDone();
emit done();
}
int KEduVocDocument::saveAs( const KUrl & url, FileType ft, const QString & generator )
{
KUrl tmp( url );
if ( ft == Automatic ) {
if ( tmp.path().right( strlen( "." KVTML_EXT ) ) == "." KVTML_EXT )
ft = Kvtml;
else if ( tmp.path().right( strlen( "." CSV_EXT ) ) == "." CSV_EXT )
ft = Csv;
else {
return FileTypeUnknown;
}
}
QFile f( tmp.path() );
if ( !f.open( QIODevice::WriteOnly ) ) {
kError() << i18n( "Cannot write to file %1", tmp.path() );
return FileCannotWrite;
}
KUrl oldUrl = d->m_url;
bool saved = false;
d->m_url = tmp;
switch ( ft ) {
case Kvtml: {
// write version 2 file
KEduVocKvtml2Writer kvtmlWriter( &f );
saved = kvtmlWriter.writeDoc( this, generator );
}
break;
///@todo port me
// case Kvtml1: {
// // write old version 1 file
// KEduVocKvtmlWriter kvtmlWriter( &f );
// saved = kvtmlWriter.writeDoc( this, generator );
// }
// break;
case Csv: {
KEduVocCsvWriter csvWriter( &f );
saved = csvWriter.writeDoc( this, generator );
}
break;
default: {
kError() << "kvcotrainDoc::saveAs(): unknown filetype" << endl;
}
break;
} // switch
f.close();
if ( !saved ) {
kError() << "Error Saving File" << tmp.path();
d->m_url = oldUrl;
return FileWriterFailed;
}
setModified( false );
return 0;
}